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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtctcgtttgtctcgtttctatcgtaagacacgcgctaaacgaggctatgtgttttgtag

Basic information

species Selaginella moellendorffii
transcript EFJ32018
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: LOC_Os08g06480.1 (Oryza sativa), 5'ss of exon 14
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtctcgtttgtctcgtttctatcgtaagacacgcgctaaacgaggctatgtgttttgtag-------------------------------------
|||| ||||| ||| | || || ||  | || ||| |||||||||||||||| ||||||  |||||| || || ||||| |||||||||||||| |||||||   |         |   |   ||||    |  |   | | ||       || |  ||| ||                                      
AAATTAAGGCATGGTTATATGACTGTTTGGGCTCAAGGGTTGACTATGATGCTCCTGGACATTGGTGTACTACCATGGCTTACAGTGCTGATGGAACAAGgtg-atgagacactgcaaatgaatatcagctgctaattgttcaagacaataatatagtttctaaaccttcacaaattaagtgaatatattgaataaatagt

upper sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 5'ss of exon 15
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtctcgtttgtctcgtttctatcgtaagacacgcgctaaacgaggctatgtgttttgtag-----------------------------
| || ||||| ||||| || |||    | || ||  | ||||||||||||||||| |||  |||||||||||||||||| || ||||| |||||  |||||||  |     || | || ||  || | | |  || | |   |||  || | |    |||||                               
AGATAAAGGCTTGGCTATATGATAATTTGGGATCCAGAGTTGACTATGATGCGCCAGGACATTGGTGCACAACAATGGCATATAGTGCAGATGGTTCAAGgttcat---aattatttctttgttagcatgattcatgtgggtaactgggtttttgtctttgttttcactgattctttttgcccttgtgagtag

upper sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: GRMZM2G042992_T01 (Zea mays), 5'ss of exon 14
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtctcgtttgtctcgtttctatcgtaagacacgcgctaa-----acgaggctatgtgttttgtag------------------
|||||||||| ||| |||| |||||| | || ||| | |||||||||||||| ||||||  |||||| || || ||||| |||||||||||||| |||||||    |              | ||  ||   | |   ||| |     |  |  |||| |   || | |                  
AAATCAAGGCATGGTTGTATGATTGCTTGGGCTCAAGAGTTGACTATGATGCTCCTGGACATTGGTGTACTACCATGGCTTACAGTGCTGATGGGACAAGgtgaaacatagcaaatgttaatataaagtttaatatctgctgatgagtaacaaactatataagttcttgatccattttttcttgcag

upper sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: GLYMA15G00880.1 (Glycine max), 5'ss of exon 14
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtt---tgt-ctcgtttgtctc-gtttctatcgtaagacacgcgctaaacgaggctatgtgttttgtag-----------------------------------
| || || || ||| | || |||    | || || || ||||| ||||| || |||||| ||||||| ||||| |||||||| ||||||||||| |||||||    | | |||   |||  |   || |||  |   |      |||   |     || | ||||                                       
AGATAAAAGCATGGTTATATGATAATTTGGGATCTCGTGTTGATTATGAAGCTCCTGGACGTTGGTGTACAACCATGGCCTATAGTGCTGATGGTACAAGgtcccatatactcaactgtggctacttgtattattgaat-tatactatctgttttgatctatttttgcccaaacatttttttttggcctgaatgtattttatag

upper sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: GLYMA13G44420.2 (Glycine max), 5'ss of exon 15
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtctcgtttgtctcgttt-------ctatcgtaagacacgcgctaaacgaggctatgtgttttgtag--------------------------------
| || || || ||| |||| |||    | || || || ||||| ||||| || |||||| | ||||| ||||| |||||||| ||||||||||| ||||||||| | |       |  |  |        ||| | |  | ||   ||        |||| | |  |  |                                 
AGATAAAAGCATGGTTGTATGATAATTTGGGATCTCGTGTTGATTATGAAGCTCCTGGACGATGGTGTACAACCATGGCCTATAGTGCTGATGGTACAAGgtttatatacccaaccatggctacttgtattattgaattatactatctgttttgatctatttttgctcaaacattttctttttggcttgaatgtattttatag

upper sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: GLYMA08G22910.2 (Glycine max), 5'ss of exon 15
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgt------ttgtctcgttt--gtctcgtttc--tatcgtaagacacgc-gctaaacgaggctatgtgttttgtag------------------------------------------
|||| || || ||| |||| ||     | || || || ||||| ||||| || |||||  ||||||||||||| ||||| || ||||||||||| |||||||      |  ||||   |  ||||| ||    |||  | || |  || |   |   |   |||   || | |                                            
AAATAAAAGCATGGTTGTATGACAATTTGGGATCTCGTGTTGATTATGAAGCTCCTGGTCGTTGGTGCACAACCATGGCTTATAGTGCTGATGGTACAAGgtaatatatattctcagctaggtctccttgtgttattttgagtcttgctgtgcagttaaattatactttcttttcataccaacgtacaaatattttttggctatgactatactacag

upper sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: Vv09s0002g08370.t01 (Vitis vinifera), 5'ss of exon 14
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtctcgtttgtctcgttt-ctatcgtaagacacgcgctaaacgaggctatgtgttttgtag---------------------------------------------------------------
| || || || ||| | || |||  | | || || || ||||| |||||||| || ||  | ||||||||||||||||| |||||||| ||||| |||||||| || |  | |  | | ||| |||  |  | |    | |   |   |    ||||      ||                                                               
AGATAAAAGCATGGTTATATGATAACTTGGGATCTCGAGTTGATTATGATGCTCCAGGTCGCTGGTGCACAACAATGGCTTACAGTGCAGATGGTACAAGgttggtttactcttacccatttgctagtgctacaagtcctcatcatttgttggtgtgccaatcagaattattgatgagtattttgatgtttaccttttctttcgggtggtgggttttcatatttacag

upper sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: Vv11s0016g05620.t01 (Vitis vinifera), 5'ss of exon 15
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgt-------------ctcgtttgtctcgtttctatcgtaagacacgcgctaaacgaggctatgtgttttgtag--------------------------------------------------
|||| ||||| ||| |||| |||  | | || ||  | ||||| |||||||| || ||   ||  |  ||||||||||| |||||||||||||| ||||||||| |              || ||  |||  ||||   | |           || | |  ||| | || | |||                                                    
AAATAAAGGCATGGTTGTATGATAACATGGGCTCTAGAGTTGATTATGATGCACCGGGTCATTCATCTACAACAATGGCATACAGTGCTGATGGGACAAGgtttttatatgacttctctttcattattctgatttcccccatttctaggtgattagaagttgctttttgctctgttatatgttgtctaactggagtatctcctaaatgatatatggacaatccatag

upper sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 14
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtctcgt-ttgtctcgt-ttctat-cgt----aagacacgcgctaaacgaggctatgtgttttgtag-----------------------------
| || || || ||||| || |||   ||||||||  | |||||||||||||| || ||   ||||||||| |||||||| ||||||||||||||||| |||| |||      |||  |||  || ||| |||    |||      | |  |     |||  || |   |                               
AGATAAAAGCCTGGCTCTATGATCTTCTTGGTTCTAGAGTTGACTATGATGCACCAGGGCATTGGTGCACTACAATGGCTTACAGTGCTGATGGCACTAGgtatgtagaaccttgattcgccttttatacgtgtcaaagttgtttggtttaattcactaaatgctccatctaaaatggatgtttgtggttgccatctgga

upper sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 14
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 14
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtc--tcgtttgtctcgtttctatcgt----aagacacgcgctaaacgaggctatgtgttttgtag------------------------------
| || || || ||||| || |||  |||||| ||  | |||||||| ||||| |||||   ||||||||| |||||||| ||||||||||| ||||| |||| |  |   | ||  |||| |||||  |||    |||  |   | |   |    |||   | | | |                                
AGATAAAAGCTTGGCTCTATGATCTCCTTGGATCTAGAGTTGACTACGATGCACCTGGTCATTGGTGCACTACAATGGCTTACAGTGCTGACGGCACTAGgtattccaaactttaatctcctttcttacgttttgaagttatttggtgtgcacaactaaacgctctatccaagatcaatgtgcgtggttttcttgtagca

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 44

AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtctcg ... tgttttgtagGCTCTTTTCGTGCGGAACTAGCAAGGAGGGTGACTCATTCCTTGTCGAGTGGAATGAAAGTGAAGGGGTTATCAAACGCACGTACATTGGATTCCGTAAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAATCAAGGCGTGGCTGTACGATTGCCTTGGTTCACGGGTTGACTATGATGCGCCTGGAAGTTGGTGCACAACAATGGCCTACAGTGCTGATGGCACAAGgtttgtctcgtttgtctcgtttctatcgtaagacacgcgctaaacgaggctatgtgttttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT